title: USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing.
abstract: Post-translational histone modifications play important roles in regulating chromatin structure and function. Histone H2B ubiquitination and deubiquitination have been implicated in transcriptional regulation, but the function of H2B deubiquitination is not well defined, particularly in higher eukaryotes. Here we report the purification of ubiquitin-specific peptidase 49 (USP49) as a histone H2B-specific deubiquitinase and demonstrate that H2B deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons. USP49 forms a complex with RuvB-like1 (RVB1) and SUG1 and specifically deubiquitinates histone H2B in vitro and in vivo. USP49 knockdown results in small changes in gene expression but affects the abundance of >9000 isoforms. Exons down-regulated in USP49 knockdown cells show both elevated levels of alternative splicing and a general decrease in splicing efficiency. Importantly, USP49 is relatively enriched at this set of exons. USP49 knockdown increased H2B ubiquitination (uH2B) levels at these exons as well as upstream 3' and downstream 5' intronic splicing elements. Change in H2B ubiquitination level, as modulated by USP49, regulates U1A and U2B association with chromatin and binding to nascent pre-mRNA. Although H3 levels are relatively stable after USP49 depletion, H2B levels at these exons are dramatically increased, suggesting that uH2B may enhance nucleosome stability. Therefore, this study identifies USP49 as a histone H2B-specific deubiquitinase and uncovers a critical role for H2B deubiquitination in cotranscriptional pre-mRNA processing events.
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Zhang
authors.forename: Amanda
authors.initials: A
authors.lastname: Jones
authors.forename: Heui-Yun
authors.initials: HY
authors.lastname: Joo
authors.forename: Dewang
authors.initials: D
authors.lastname: Zhou
authors.forename: Ying
authors.initials: Y
authors.lastname: Cao
authors.forename: Shaoxia
authors.initials: S
authors.lastname: Chen
authors.forename: Hediye
authors.initials: H
authors.lastname: Erdjument-Bromage
authors.forename: Matthew
authors.initials: M
authors.lastname: Renfrow
authors.forename: Hang
authors.initials: H
authors.lastname: He
authors.forename: Paul
authors.initials: P
authors.lastname: Tempst
authors.forename: Tim M
authors.initials: TM
authors.lastname: Townes
authors.forename: Keith E
authors.initials: KE
authors.lastname: Giles
authors.forename: Ligeng
authors.initials: L
authors.lastname: Ma
authors.forename: Hengbin
authors.initials: H
authors.lastname: Wang
mesh_terms: D000074183:ATPases Associated with Diverse Cellular Activities; D048868:Adaptor Proteins, Signal Transducing / Q000378:metabolism; D002352:Carrier Proteins / Q000378:metabolism; D045744:Cell Line, Tumor; D004265:DNA Helicases / Q000378:metabolism; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D006367:HeLa Cells; D006657:Histones / Q000378:metabolism*; D006801:Humans; D060588:LIM Domain Proteins / Q000378:metabolism; D046988:Proteasome Endopeptidase Complex; D012322:RNA Precursors / Q000378:metabolism*; D012326:RNA Splicing; D014157:Transcription Factors / Q000378:metabolism; D043222:Ubiquitin Thiolesterase / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*; D054875:Ubiquitination
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D002352:Carrier Proteins; D006657:Histones; D060588:LIM Domain Proteins; C092282:PSMC5 protein, human; D012322:RNA Precursors; D014157:Transcription Factors; C571993:USP49 protein, human; D043222:Ubiquitin Thiolesterase; D046988:Proteasome Endopeptidase Complex; D000074183:ATPases Associated with Diverse Cellular Activities; D004265:DNA Helicases; C486549:RUVBL1 protein, human
keywords: H2B deubiquitination; USP49; pre-mRNA splicing; transcription